Tertiary structure characterisation

Tertiary Structure Characterisation by Chemical Modification and Mass Spectrometry... 

When proteins fold into their tertiary structures, there are often subdivisions within the protein, designated as domains, which are characterised by similar features or motifs. A protein domain is a part of the protein sequence and structure that can evolve, function and exist independently of the rest of the protein chain. Many proteins consist of several structural domains. One domain may appear in a variety of evolutionarily related proteins. Domains vary in length from about 25 up to 500 amino acids. The shortest domains, such as zinc fingers , are stabilised by metal ions or disulfide bridges. Domains often form functional units, such as the calcium-binding EF hand domain of calmodulin. As they are self-stable, domains can be swapped by genetic engineering between one protein and another, to make chimera proteins. 

Polyethylene is a man-made homopolymer. Its chemical synthesis is well understood. It is a random walk polymer with little secondary or tertiary structure. A batch can largely be characterised by its molecular weight distribution, and its rheology can be related to these parameters by developed rules of polymer behaviour. The action of specific chemicals as plasticisers can be used to modulate these bulk properties in a predictable way, allowing the nature and characterisation of its glass to fluid transition to be predicted. 

Previously, we have examined the formation of amino acid hydroperoxides following exposure to different radical species [100]. We observed that valine was most easily oxidised, but leucine and lysine are also prone to this modification in free solution. Scheme 12 illustrates the mechanism for formation of valine hydroperoxide. However, tertiary structure becomes an important predictor in proteins, where the hydrophobic residues are protected from bulk aqueous radicals, and lysine hydroperoxides are most readily oxidised. Hydroperoxide yield is poor from Fenton-derived oxidants as they are rapidly broken down in the presence of metal ions [101]. Like methionine sulphoxide, hydroperoxides are also subject to repair, in this case via glutathione peroxidase. They can also be effectively reduced to hydroxides, a reaction supported by the addition of hydroxyl radical in the presence of oxygen. Extensive characterisation of the three isomeric forms of valine and leucine hydroxides has been undertaken by Fu et al. [102,103], and therefore will not be discussed further here. 

Beyond the characterisation of primary structures, the direct analysis tertiary structure states and even non-covalent supramolecular complexes by mass spectrometry have not been considered feasible in previous work. In a few cases tertiary structure-dependences have been found, e. g. specific fragmentations in FAB mass spectra of a-helical polypeptides and some MALDI and PD mass spectra of proteins suggesting some native-like structure of macromolecular ions [106, 107]. This situation has changed drastically recently with the analytical development of ESI-MS. A substantial number of ESI-MS studies have demonstrated the identification of supramolecular complexes of biopolymers, as well as specific non-covalent complexes with low-molecular weight constituents [15—18, 31]. In contrast to other ionisation methods in which, predominantly, singly charged ions are produced (EAB,... 

Most solid peroxochromates explode when heated or struck, some are reported to explode spontaneously at room temperature. Few have been isolated and fully characterised. Assigned structures are sometimes doubtful [1], especially when questionable primary sources have been reinterpreted by secondary and tertiary... 

If the successive vertical lines are located alternately on the opposite sides of the horizontal line, above and below it, in the adapted Fischer projection, or if the successive alkyl substituents appear alternately in front of and behind the plane of the extended polymer backbone in the flat zigzag projection (Figure 3.1), then a syndiotactic poly(a-olefin) structure occurs. These two representations show that the syndiotactic polymer contains neighbouring tertiary carbon atoms of opposite relative configurations. The syndiotactic poly (a-olefin) chain is characterised by the appearance of stereodiads of the opposed relative... 

Isotactic poly(x-olcfin)s crystallise in a helical conformation, and, in the case of polypropylene, with three units per turn [4,5], Isotactic polypropylene has a melting point of 175°C and does not dissolve in boiling n-heptane [6,7], Note that, depending upon the configuration of the tertiary carbon atom of the polymer main chains, the poly(x-olefin) helices will be characterised by right-handedness or left-handedness. It should be mentioned that the helical structure of the poly(x-olcfin) chain per se is sufficient for the appearance of chirality of such a macromolecule [8], Figure 3.3 presents the helical conformation of chains of isotactic poly(a-olefin)s in the crystalline state (with three units per turn - the case of polypropylene) [5],... 

It should also be mentioned that atactic polymers may be formed from monodeuteropropylene and pentadeuteropropylene, similarly to the case of the polymerisation of non-deuterated propylene. However, atactic structures with respect to one stereogenic tertiary carbon atom, with the other possibly arranged to form tactic polymer sequences, are not known. Also, ditactic polymers, which might be characterised by the appearance of two distinct series of tacticity as regards both stereogenic tertiary carbon atoms, i.e. the isotactic with respect to one stereogenic carbon atom and syndiotactic with respect to the other one, and vice versa, are not known. 

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